1. Turn on 3DS
2. Run emuNAND9 (if you don't have it, get it here)
3. Unmount SD card with select, insert new card
4. Format your SD card for emuNAND
5. Turn off 3DS
6. Put old SD card in computer
7. Backup your emuNAND partition (using this)
8. Put new card in computer
2. Restore it to the new card (using this)
3. Copy all files to the new card
4. Play some games

NOTE: If your SD card is >32GB, use this to format it to FAT32 before anything else